AMBER Archive (2005)

Subject: AMBER: PBCAL=0. Problems in MM/PBSA

From: Javier Perez Miron (javier.perez_at_uab.es)
Date: Thu Jan 13 2005 - 14:41:29 CST

Hello amber users,

I have a problem with my MM/PBSA calculations.

When I do the calculation using MM/GBSA (without Delphi), I obtain a value of
GB that it is not 0.0. So, the MM/GBSA calculation goes right.

Nevertheless, when I run a MM/PBSA using AMBER7 and Delphi, I obtain the value
of PBCAL is 0.0.

The delphi.log files that I obtain are like this:

(my system has 150 atoms)

___________________________________________________
  ___________________DelPhi II____________________
 / \
 | A program to solve the PB equation |
 | in 3D, using non-linear form, incorporating |
 | 2 dielectric regions, ionic strength, periodic |
 | and focussing boundary conditions, utilizing |
 | stripped optimum successive over-relaxation |
 | and an improved algorithm for mapping the |
 | Mol. Surface to the finite-Difference grid |
 \__________________ ____________________/
                     DelPhi II

  program started on Thu Jan 13 2005
              at 19:02:57
 opening parameter file delphi.prm.0
 atom radii read from file
 ./HHH.siz2

 !my siz based on PARSE
 !(value for P taken from Pauling,
 ! for Mg from Biophys J 2001, 80, 1151)
 # of radius parameter records: 150

 atomic charges read from file
 ./HHH.crg2

 ! Amber parm99 charges
 # of charge parameter records: 150
 assigning charges and radii...

 opening formatted file:fort.13
 number of atoms read in = 0

 exiting due to non-existence of atom file

_______________________________________________

I have read Delphi manuals and I know that fort.13 is a file with pdb format.
I've read in AMBER7 manual about mm/pbsa and it doesn't talk about we have to
use a pdb file in mm_pbsa.in.

Maybe there are some bugs in the mm_pbsa.pl I have (ver. 1/16/2002 ). Do you
know if there is a new version of mm_pbsa.pl ?

If someone can help me, I accept any suggestion.
Thanks in advance,

Xavi

Javier Perez

Grup de Química Orgànica Estructural
Departament de Química
Universitat Autònoma de Barcelona
08193 Bellaterra-Espanya
Lab.: C7-455
Tel.: +34 935811266
http://einstein.uab.es/cjaime/
http://www.gratisweb.com/xavip/

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